Indian Red Jungle fowl depicts close genetic relationship with Indian native chicken breeds as evidenced through whole mitochondrial genome intersection

Abstract Native chickens are dispersed in a wide range of geometry and they have influenced hereditary assets that are kept by farmers for various purposes. Mitochondrial DNA (mtDNA) is a widely utilized marker in molecular study because of its quick advancement, matrilineal legacy, and simple molecular structure. In a genomics study, it is important for understanding the origins, history, and adjustment of domestication. In this report, for the first time, we utilized Next-generation sequencing (NGS) to investigate the mitochondrial genomes and to evaluate the hereditary connections, diversity, and measure of gene stream estimation in seven Indian native chicken breeds along with twenty-two Asian native breeds. The absolute length of each mtDNA was 16775bp harboring 4 tRNA genes, 2 rRNA genes, 12 protein-coding genes, and 1 D-loop region. The chicken breeds were genotyped by using the D-loop region and 23 haplotypes were identified. In addition, when compared to only Indian native breeds more haplotypes were identified in the NADH dehydrogenase subunit (ND4 and ND5), Cytochrome c oxidase subunit (COXI and COXII), Cytochrome b, mitochondrial encoded ATP synthase membrane subunit 6, and Ribosomal RNA genes. The phylogenetic examination utilizing N-J computational algorithms indicated that the analyzed all native chicken breeds were divided into six significant clades: A, B, C, D, E, and F. All Indian native breeds are coming under the F clade and it says all Indian breeds are domesticated in India. Besides, the sequencing results effectively distinguished SNPs, INDELs, mutations, and variants in seven Indian native breeds. Additionally, our work affirmed that Indian Red Jungle Fowl is the origin of reference Red Jungle Fowl as well as all Indian breeds, which is reflected in the dendrogram as well as network analysis based on whole mtDNA and D-loop region. Albeit, Indian Red Jungle Fowl is distributed as an outgroup, proposing that this ancestry was reciprocally monophyletic. The seven Indian native chickens of entire mtDNA sequencing and disclosure of variations gave novel insights about adaptation mechanisms and the significance of important mtDNA variations in understanding the maternal lineages of native chickens.